Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_028320915.1 H567_RS0107410 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000422285.1:WP_028320915.1 Length = 291 Score = 157 bits (398), Expect = 2e-43 Identities = 102/296 (34%), Positives = 165/296 (55%), Gaps = 17/296 (5%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M+ FLQ L+ G+ G +YGLI +G +++ G++G+IN AHG++ M+ + ITF+ L Sbjct: 1 MDVFLQTLVAGILKGGLYGLIGMGMSLIMGVMGIINLAHGQLMMVAMY---ITFVCFTYL 57 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAP---LISAIGMSIFLQNY 117 G+ P A L++ + ++ + G ++R A PL L P ++ +G+ + L Sbjct: 58 GLD--PYAALLITMPALF---LLGALIQRYALNPLMEVESLLPENQVLMTVGIGMVLTEI 112 Query: 118 VQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMY-GFT-QLITRTSLGR 175 + + + K +Q + + G +S+ T IAL++ GF + +T LGR Sbjct: 113 ARFIFSSDYKSVQTAYSSSSFFLRG---ISFSVALTAAFFIALLFTGFMFWFLLKTDLGR 169 Query: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKA 235 A RA QDK A L+GV+ R+ LTF +G+AL A AG +++ IY + IG KA Sbjct: 170 AIRATAQDKDAALLMGVDAKRITILTFGIGSALVAAAGTLLMPIYYLFP-DIGSPFTRKA 228 Query: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTG 291 F +LGG+GS GA+ GG+ +GL EAF + Y+G + D+ I +LVL+F P+G Sbjct: 229 FVITILGGLGSTVGAIFGGLTLGLAEAFGATYIGMAFDDMIGLLIFILVLLFLPSG 284 Lambda K H 0.329 0.144 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 283 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 291 Length adjustment: 26 Effective length of query: 275 Effective length of database: 265 Effective search space: 72875 Effective search space used: 72875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory